br2013,
First of all, it’s best to use MyEclipse 2013 (Juno) for Maven. We have made a lot of enhancements in that area since MyElipse 10.x (Indigo).
If you are managing projects through parent poms you might experience missing dependencies errors if you don’t include all of the projects. You can try closing projects you don’t want to use after importing them into the workspace.
You can make changes in parent project and children ones. The structure of Maven project on disk is usually hierarchical, so children projects are contained inside of the directory with parent pom. They are imported from those locations into workspace, so you can see some projects listed under parent project and as a separate project.
Let us know if you have more questions!